The fish genus Rastrelliger is composed of three morphologically recognized species; Rastrelliger kanagurta, Rastrelliger brachysoma and Rastrelliger faughni. In this study, cytochrome b gene sequencing was applied to address the systematics and phylogenetic relationships of these species. In agreement with previous morphological data, the results corroborate monophyletic discrimination between all the species. However, inconsistent bootstrap support (< 50 to 88%) between R. kanagurta and R. brachysoma was observed indicating limited divergence between these two species. R. faughni is recognized as the most basal species for this genus with high statistical support (99 and 100%). Diversification of Rastrelliger might have happen in two epochs, Miocene and early Pleistocene